HYLODE / HyStakes

Bayesian modelling for Healthcare

HyStakes

Installation

Mac OS (First run)

• Install Quarto
• Install the VSCode extension for Quarto
• Clone the repo at the command line

git clone https://github.com/HYLODE/HyStakes.git
cd hystakes
make dev_mac_os_first_run
direnv allow

Development work

• Open VSCode in the hystakes directory
• You may(?) need to specify the Python kernel. This should be the one from the hystakes conda environment. To do this on Mac, type command-shift-P to bring up VSCode's command palette, then search for Python Interpreter, then pick the HyStakes interpreter from the dropdown list of options.
• Navigate to the example files and confirm that they render correctly by following the Quarto instructions for VSCode

Developing code

Developing documentation

We assume the primary documentation will delivered through a website. A local webserver can be started to preview the work in progress. All files (.qmd, .ipynb, .Rmd, .md etc.) within the ./hystakes sub-directory will be rendered.

quarto preview

The live preview will not show global changes. You must run quarto render to see the site before you deploy.

The actual site is automatically built using github actions. Anything pushed to the main branch will be rendered (as per the rules in ./hystakes/_quarto.yml) and published to https://hylode.github.io/HyStakes/. Note that the main branch is protected and so a pull request will need to be created and approve before the site can be built. Guidance on this can be found at The Turing Way, and this tutorial.

PyMC installation

and installed version 4 via https://github.com/pymc-devs/pymc3 and got the local example working https://www.pymc.io/projects/docs/en/latest/learn/core_notebooks/pymc_overview.html